Sodium in PDB 7grw: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19, PDB code: 7grw was solved by C.-Y.Huang, A.Metz, M.Sharpe, A.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.94 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.94, 100.67, 104.39, 90, 90, 90
R / Rfree (%)	19.4 / 23.9

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19 (pdb code 7grw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19, PDB code: 7grw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:59.3 occ:1.00 O A:GLY120 2.5 33.6 1.0 O A:MET17 2.7 22.9 1.0 O A:DMS501 3.1 57.0 1.0 O A:HOH737 3.3 40.8 1.0 C A:GLY120 3.5 40.2 1.0 S A:DMS501 3.6 72.6 1.0 N A:GLY71 3.6 44.1 1.0 C A:MET17 3.7 28.6 1.0 CA A:GLY120 4.2 31.8 1.0 CA A:VAL18 4.2 27.7 1.0 CA A:GLY71 4.3 43.9 1.0 N A:VAL18 4.4 27.2 1.0 N A:SER121 4.4 27.1 1.0 CA A:SER121 4.6 36.5 1.0 C A:ALA70 4.6 41.9 1.0 C1 A:DMS501 4.6 43.1 1.0 CA A:ALA70 4.7 34.3 1.0 CB A:MET17 4.7 23.6 1.0 CA A:MET17 4.8 30.4 1.0 O A:GLN69 4.9 33.9 1.0 C A:VAL18 4.9 30.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-19 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:39.5 occ:1.00 OD1 B:ASP263 2.3 39.1 1.0 O B:HOH706 2.3 35.0 1.0 O B:PHE223 2.3 30.1 1.0 OD1 B:ASN221 2.4 33.4 1.0 O B:ASN221 2.5 23.9 1.0 O B:ASP263 3.1 35.8 1.0 C B:ASN221 3.3 31.5 1.0 N B:PHE223 3.3 32.0 1.0 C B:PHE223 3.4 35.5 1.0 CG B:ASP263 3.5 44.0 1.0 CG B:ASN221 3.6 37.6 1.0 N B:ASN221 3.8 43.3 1.0 CB B:ALA266 3.9 47.6 1.0 CA B:PHE223 3.9 29.3 1.0 C B:ASP263 3.9 43.7 1.0 CA B:ASN221 4.0 33.8 1.0 C B:ARG222 4.0 31.0 1.0 N B:ARG222 4.1 34.0 1.0 CA B:ASP263 4.2 45.0 1.0 OG B:SER267 4.3 33.1 1.0 OD2 B:ASP263 4.3 47.6 1.0 CB B:ASN221 4.4 31.6 1.0 CB B:ASP263 4.5 42.2 1.0 CA B:ARG222 4.5 35.7 1.0 CB B:PHE223 4.5 30.8 1.0 ND2 B:ASN221 4.5 33.1 1.0 N B:THR224 4.5 30.8 1.0 N B:SER267 4.7 30.9 1.0 O B:ARG222 4.8 32.4 1.0 CA B:ALA266 5.0 39.0 1.0 C B:LEU220 5.0 32.2 1.0

C.Y.Huang, A.Metz, R.Lange, N.Artico, C.Potot, J.Hazemann, M.Muller, M.Dos Santos, A.Chambovey, D.Ritz, D.Eris, S.Meyer, G.Bourquin, M.Sharpe, A.Mac Sweeney. Fragment-Based Screening Targeting An Open Form of the Sars-Cov-2 Main Protease Binding Pocket. Acta Crystallogr D Struct V. 80 123 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38289714
DOI: 10.1107/S2059798324000329